Specimen 343
by Tturttwig
Summary: AU Sonic. Sonic leaves a government security force after a change of heart. Feedback appreciated.
1. Rogue

Disclaimer: This is fanfiction. Sonic the hedgehog franchise and it's characters belong to Sega and its partners.

Part 1

-

The city lights darkened the stars in the sky, leaving a black void. At the center of that light stood a building stretching hundreds of feet taller than any of the other skyscrapers. Chaos Containment rolled across the its top in brilliant white light. Even in the darkness of night, the city roared with noise. So not many people heard the sound of glass breaking as a blue blur crashed out a window.

A blue hedgehog in red sneakers and a gray helmet shot out into the air. His gray vest blew into the wind as he threw it off. Then he landed on top a building with a crunch. The cement building cracked slightly, but was still stable.

A voice came from the helmet. "Sonic. What are you doing!?"

Sonic spoke into an earpiece. "I'm done." He took off the helmet throwing it to the ground. He clenched his fists looked at the helmet in disgust. Then he looked at his hands. "Never again."

Sonic ran jumping from roof to roof, his hair blown back by the wind. He shot across the city leaving dust and wind so strong it blew over dumpsters and ripped nearby flags. He kept going as the city skyline blurred into the distance, not stopping until the road turned to dirt.

He looked back at the city lights one last time sighing. "Goodbye Ivo." Then he darted across fields of grass and disappeared into a forest.

Back at the Chaos Containment building, a puggy scientist with a thick brown mustache a red lab coat looked out from the broken window. He wore blue tinted goggles, which he took off to reveal deep brown eyes. His face was grief stricken as he stared out into the city.

Two government agents in black suits ran up to him and saluted. "Sir. We came as soon as we heard the alarm. What's going on?" They both gaped when they saw the shattered window.

The scientist sighed. "I don't know. Sonic just jumped out the window and removed his communicator."

"What!?" One of the men spoke into an earpiece. "Headquarters! We have a containment breach! Specimen 343 has gone rogue!"

"Copy that Agent Larz. We'll send out a strike force now. Do you have a visual of his trajectory?"

Agent Larz looked through the broken window for the nearest building. "Looks like 34 degrees west of south.

"We are sending strike force 34 degrees west of south. Do you confirm?"

"Yes." Agent Larz stepped back from the window. Boom! An explosion sounded from a lower floor.

The floor shook, sending the scientist to the floor as fire alarms went off. "What was that!?" He got up looking around.

Agent Larz motioned to him. "Sir. We need to get you to safety immediately."

"Right." The scientist looked at Agent Larz, then back to at the missing window bewildered. "Sonic. What have you done?" He walked away with the two agents.

-

Part 2

-

A young yellow fox with two tails lay on a bed looked at the metal walls in front of him. Light streamed from a window reminding him of the outside world. He turned toward the bars to cell, then back to the marks he'd made on the wall. He'd written down twenty three on the wall in his time here, twenty three days, trapped in an impenetrable prison with the rest of the failed experiments.

He'd been laying there for a few hours and was half asleep when a boom sounded in the distance. Hot wind blew down the hallways and the young fox ran to see what was happening. A blue object shot down the hall, stopping in front of his cell. Then it turned into a giant hedgehog wearing red sneakers and gloves. The hedgehog looked at the young fox. "Hey kid, it's Tails right? You wanna get out of here?" It pulled out keys swinging them around its finger whistling.

"What!? Are you for real!?" Tails raised an eyebrow. "Wait, how do you know my name?"

"I read it in your file." The hedgehog unlocked the cage. "Now come on. The guards will be on us soon."

"Ok." Tails nodded following the blue hedgehog down the stone hallway. They ran past several cells as different animals looked at them cursing or asking for help. "Wait. There are others trapped here too."

"I know they don't look like it, but the guys here are locked up for a reason. The only innocent one here is you." The hedgehog said.

Tails looked back at the prisoners, but then faced forward again. Tails and the hedgehog ran into a few offices with guards shooting at them. But the bullets didn't even come close to them as the hedgehog to blink in and out of view every so often. Eventually they made their way out to a courtyard and a wire fence. A guard looked down at them from a tower and yelled, but then he fell on his butt and didn't get up.

Tails stared at the guard horrified. Then the hedgehog smiled at him. "Don't worry. He's just knocked out. He'll be fine. No come on." It waved Tails toward a hole in the fence and the two ran as the prison behind them went up in smoke.

Tails glanced back and stopped when he saw the black cloud coming from the building. "Wait, that's a fire!"

"No. It's just smoke bomb. Incredible annoying and hard to see through, but perfectly safe." The hedgehog kept running and Tails followed after him into a thick oak forest. As they ran, the hedgehog looked over at him. "So, you know of any place to hide?"

"Huh? Oh. Yeah maybe. Follow me." Tails ran toward an area where the trees started turning to aspen and came to a stream with a cave behind it. "We should be safe here."

"Ok. Good." The hedgehog looked at the cave. "Just let me do the talking."

"Yeah. Just let me do any talking. Knuckles doesn't like strangers." Tails said. The hedgehog grimaced and Tails looked at him confused. "What's the matter?"

"Nothing, it's fine." The two walked into the cave, darkness enveloping them with each step. Soon it was pitch black. But then bits of light started to stream in. As they went further, the light grew brighter into the form of a fires on torches.

Tails and the hedgehog kept going until they saw a red echidna looking at Tails. "Kid. You're ok!" He ran up to Tails. "What happened?"

"I was trapped in a prison. This hedgehog helped me escape." Tails smiled looking at the hedgehog. "Say, I never got your name."

Knuckles glared at the hedgehog. "You…I don't need a name."

The hedgehog grimaced. Tails looked between the two of them confused. "Wait, what's going on?"

"Tails you idiot! How could you bring Sonic here!!?" Knuckles clenched his fists.

"What!?" Tails looked in horror. He'd just brought a government agent to his friends.

Knuckles walked over to Sonic. "Guess I'd have to fight you sooner or later." He looked at Tails. "Get out of here before he kills you."

-

Part 3

-

An old man in a police uniform sat in a well lit room with steel gray walls and windows with a view of the city skyline. He was scrolling through a computer file when the door opened.

A man in a red lab coat stepped into the office. "Chief Oran. You wanted to see me sir?"

"Ah. Dr. Robotnick. Thank you for meeting with me on such short notice." Chief Oran turned off the computer screen.

"I assume this is about specimen 343?" He asked.

"Yes. Sonic, going rogue has been problematic. Morale is down, and now people are wondering where their celebrity superhero is." Oran sighed looking out the window. "I still don't understand why one of our best agents went rogue like that. Wasn't he programmed to be obedient?"

"Well, yes. But it's not that simple, he's not a robot." Dr. Robotnick shook his head.

The chief raised an eyebrow. "Well, ok, cyborg. Whatever. I thought that chip could override his free will if he became dangerous."

"He's flesh and bone. It's true the programming should have made him completely obedient, but he's always had more personality than a machine." Robotnick looked at the skyline. "Still...I never imagined he would turn on us."

"He did more than that." Oran slid a photo over to Robotnick.

He looked at the photo. It showed Sonic running from an exploding building with what looked like a yellow two tailed fox behind him. Robotnick's eyes widened as he read the name of the building. "Argon Prison! The people there are the worst criminals imaginable! Why would he destroy that place!?"

"We don't know. The strike force hasn't been able to track him down yet. As much as I hate to admit it. You may have created the most powerful weapon in the world."

"So I'm responsible for a prison break of the most dangerous criminals in the world." Dr. Robotnick gritted his teeth. "What have I done?" He stared at the man intensely. "How many people?"

"For now, we've had no deaths, and only one prisoner escaped. But we need a way to stop him. Conventional methods haven't worked, and we can't just launch a nuke at him." Oran sighed.

"Why not send out Metal?"

"Metal? Isn't he still in the experimental stages?"

"Yes. But given current circumstances, I think we should at least consider it. Though I understand hesitation with the possible risk to the public." Robotnick pulled out a computer drive from his coat, handing it to Oran. "This has everything we know about Metal so far."

Oran plugged the drive into his computer, turning the screen on. "All right. I'll take a look at it. But for now, I need you to do whatever you can to stop Sonic. And find out why he turned on us."

"I've already started looking into it. Hopefully I can find some answers soon." Robotnick stood up, exiting from the room.


	2. Trial

Part 1

-

Knuckles stared at Sonic, sweat pouring down his face. "If you've come here to kill me, let's get this over with."

Sonic raised his hands. "I don't want to fight you." A sad look ran across his face.

"Right…" Knuckles slowly approached Sonic, then lunged. Sonic rolled to the side as Knuckles punched through the cave wall. Dust flew and he jumped at Sonic again. Sonic dodged again and again. As the two kept fighting, parts of the cave walls came down around them.

Soon they were completely surrounded by rock wall. Sonic looked around, then back at Knuckles. "What's the point of trapping us in here?"

Knuckles smiled at Sonic. "I won't let you hurt my friends. So neither of us is getting out of here."

Sonic sighed. "So this is what you're willing to do to trap me." He sat down sighing and looked at the walls. "Guess we can at least talk now, without you being worried." A blue glow came from Sonic's chest lighting up the cave.

Knuckles eyes went wide. "Wait! You let me trap you!?"

"Yeah." Sonic nodded.

Knuckles stared for a few moments in disbelief, then grabbed him, lifting him against the wall. "Why!?"

Sonic didn't even try to fight back. "Because it's the only way we can talk without a fight apparently." He looked down. "Guess that's my fault though."

"What is this, villains' therapy? Why aren't you fighting back!?" Knuckles let go turning away. "Guess I can let my guard down, now that we're both dying in here anyway"

Sonic looked at Knuckles. "Sacrificing yourself to protect Tails. You really are as brave as I remember. Just wish you weren't so stubborn."

"What!?" Knuckles turned back to Sonic ready to attack.

Sonic raised his hands. "Look. I came here to talk. That's all. Like I said, I don't want to fight you."

-

Part 2

-

Chief Oran walked into a room with white tile floors and walls. Fluorescent lights on the ceiling bathed the machinery in white light. Plastic containers held different creatures and robots, showing readings for temperature, time span, heart beat, and electric output among other things.

Dr. Robotnick looked over a large cylindrical container with a black and red hedgehog inside. He looked up when he saw Oran. "Uh, chief sir. You wanted to see Metal right?"

"Yeah. I wanted to see this robot of your's before sending it out in public." Oran walked over and Robotnick took him over to a square plastic box with a glass on the front. At the top of the door a label read Metal Sonic. Inside was a hedgehog looking robot with a blue head and glass lenses instead of eyes. Sleek gray metal arms came off a round body. Underneath were metal legs with wheels at the bottom of blue feet.

Dr. Robotnick pulled out a remote. "This allows us to turn Metal on and off, as well as open his containment unit."

Oran sighed. "Yes. I already read the files. I know about its 2 hour battery life and its fail safe."

Robotnick laughed, somewhat embarrassed. "Right, of course. I'll just activate Metal for you then." He clicked the remote and the door to the containment unit opened. The lense eyes of the robot glowed red as sound came from the hydraulics pistons activating and gears moving.

It stepped out of the containment unit and faced Dr. Robotnick. "Metal Sonic model 1 activated. Authorized user recognized: Dr. Robotnick. What are your orders?"

Robotnick looked at the robot and spoke. "Recognize new authorized user: Chief Oran." He then gave Oran the remote.

Oran pressed a green cross shaped button on the remote and faced Metal Sonic. Metal Sonic scanned Oran and spoke again. "User confirmed: Chief Oran."

Oran raised an eyebrow. "Metal Sonic. Find Dr. Lancert."

"Objective accepted." Metal Sonic whirred for a few seconds, then spoke. "Dr. Lancert is 20 feet away horizontally, and 30 feet away vertically. Do you want Dr. Lancert brought here?"

Oran looked at Metal Sonic. "No. Have her killed." Robotnick turned to Oran startled.

Metal Sonic whirred for a few seconds. "Dr. Lancert has not been confirmed for death row, so killing her would be against standard police protocol. Objective denied."

Oran smiled at Dr. Robotnick. "Ok. I think this thing is safe to use." He turned back to Metal Sonic. "Track down Sonic, and bring him back incapacited but alive."

"Objective accepted. Specimen 343: Sonic the hedgehog will be neutralized and returned for questioning." Metal Sonic walked out of the lab.

Dr. Robotnick pressed a button on his lab coat sending down a large screen. It showed a camera view going through the lab, then through doors, hallways, stairs, and eventually the 4th Street. As it picked up speed, the surroundings blurred gray together until the color around changed to green.

Dr. Robotnick smiled. "I've taken the liberty of setting up a system so you can watch Metal's body camera from your computer.

Oran nodded. "Good. This thing seems safe. But I still can't help feeling concerned about this." He took out a roll of paper from his pocket with a list. "Still, we can't just let criminals go unpunished. Maybe this robot can deal with criminals like Sonic did."

-

Part 3

-

Knuckles' laughter boomed through the walls. "You really expect me to believe you changed sides?" He lay on the ground unable to breath.

Sonic looked at him. "No, I don't. Guess at this point, I expect to die down here."

"Yeah." Knuckles smiled. "I can't believe it. I stopped Sonic. My friends don't have to be afraid anymore, they're safe."

Sonic shook his head. "You realize they'll just send others right? Chaos Containment won't stop. They'll just keep hunting you until they capture you."

Knuckles lay there peacefully. "So what's it like working for those maniacs."

"They're not maniacs. They try to keep peace and protect innocent people." Sonic sighed looking at the rock wall. "Sometimes they go too far. That's why I left."

Knuckles shook his head laughing. "Even now you try to keep up appearances. We're dead anyway and no one will ever hear us. What was that?"

Knuckles looked around hearing some sort of banging nearby. Sonic stood up and the two followed the sound as it grew louder and louder. Sonic's eyes went wide. "Look out!"

He tackled Knuckles to the ground as a robotic hedgehog burst from the rock wall. Dust went flying and the cave shook.

The robot looked at Sonic. "Specimen 343. You are under arrest for crimes involving property damage and insubordination." Then it looked at Knuckles. "Criminal identified: Knuckles the Echidna. Secondary objective created. Knuckles, you are under arrest for crimes including property damage, assault of officers, and theft. Any attempts to resist will result in use of force."

"What the!?" Knuckles got to his feet. "What is that thing!?"

"Ivo...you sent Metal out!?" Sonic looked at Knuckles. "We need to destroy that thing before it kills someone!"

"Gladly!" Knuckles charged Metal Sonic, punching it backwards. Small dents were starting to form on it.

Then Metal Sonic's body started sending off steam and glowing red and orange. Knuckles hit it, and yelped jumping back. "Agh. That burns."

Metal Sonic walked toward Knuckles. "Do not resist. Attempts to do so will result in use of force."

The super heated robot kept walking toward Knuckles until Sonic kicked it. "Hey. I'm the one you're after!" He wagged his finger. "But I guess that doesn't matter when you're too slow."

Knuckles jumped through the hole Metal Sonic had made as it faced Sonic. "Specimen 343, submit to arrest for retrieval, interrogation, and decommission."

Sonic laughed. "Like I'm gonna turn myself to be tortured and then killed." He jumped to a rock wall and kicked off, shooting into the hole. Then he sprinted.

Metal Sonic shot out after him as he caught up to Knuckles who held his head after running into a wall. Sonic looked at him waving him on. "Come on! Follow me!"

Knuckles chased after Sonic as the two ran out of the cave. Then Knuckles glared at him. "Sonic...I'll make you pay for this."

"We've got bigger issues right now." Sonic looked at the cave as Metal Sonic came out.

Its eyes focused on Sonic for a moment, then turned to Knuckles. Fire shot out from its back as it shot at Knuckles. Sonic looked and dove, knocking him out of the way.

Metal Sonic hit Sonic back several feet as he yelled in pain. His body hit the ground and moved limply. Metal Sonic turned away from Sonic hitting Knuckles' fist.

The robot's body cracked as it fell over. Knuckles hit it with another punch as it got up. Bits of jagged metal stuck out as sparks shot off. Then it shot away. Knuckles smiled. "When are humans gonna learn. Nature beats machines every time."

Knuckles turned toward Sonic who was holding his stomach. Then he shook the head. "Why'd you do that?"

"That thing would've killed you." Sonic spat out mucus mixed with blood.

"Right." Knuckles looked toward the river. "You know I could just drown you and be done with it."

Sonic laughed, gritting his teeth to sit up. "Maybe. But I'm willing to bet you won't."

Knuckles sighed, sitting down. "No. I guess I won't."


	3. Aftermath

-

Part 1

-

The lab buzzed with noise as Dr. Robotnick worked on repairing Metal Sonic. Chief Oran had made Metal Sonic's repair his top priority with specimen 343 out and about. An assistant with red hair and freckles handed him a microchip and he inserted it into the robot's chest cavity. He covered up the chip and kept moving along the body to fix any other major malfunctions. Then he booted up Metal Sonic for a self diagnostic.

System online. Current status shows no damage to core processor or internal battery. Camera function is not operant in one eye. Piston system in need of chamber replacement. Estimated time for repairs needed to provide full function, 1 week.

Robotnick sighed. "This is a problem. If we don't have a way to combat specimen 343, I don't know how effective our damage control can be." He looked at the assistant. "Any ideas James?"

"Perhaps we could attempt use of specimen 344?" James said.

Dr. Robotnik shook his head. "No. That's way too dangerous. We don't even know if its internal battery is stable yet. What if it explodes? Or even worse, what if it works and they turn out like specimen 343?"

James nodded. "Well, what about altering specimen 343's microchip. Could that work?"

"His microchip? James, I would love to be able to do that. But someone getting close enough to do that would be suicide. I can't risk any more lives like that."

"Well, what about the fail safe? That operates at a 10 meter range."

"The fail safe?" Robotnick thought for a few moments. "Wait a minute." He rummaged through his lab coat until he pulled out a controller. "James. You designed the fail safe system, how far can you make the range with this remote?"

"Well, the signal's based on radio waves. But it really depends on the power source. The more power available the stronger the signal. The remote can handle about 150 volts without damage. That would give it a range of about 500 meters, but only for one signal. How much energy could you store in a 45cm3 area?"

"Hang on let me check." Dr. Robotnick walked over to a computer and brought up a list of materials. "Let's see...iron, steel, silver, lithium...there! 150 volts. Lancert's new lithium compound should do the trick. Didn't realize she's already finished testing." He looked up from the screen. "James, would you get Dr. Lancert?"

"You got it Doc."

-

Part 2

-

Fire lit up a cave as Sonic lay in a bed made of hay. Bandages stained red covered his stomach, and he winced from the pain as he sat up.

He saw Knuckles mixing a black liquid in a wooden bowl. "What is that stuff?"

"Special recipe. Should get you back on your feet." Knuckles dropped some green leaves in and grinded them with a wooden spoon.

"Huh, never took you for a medic." Sonic shook his head laughing.

Knuckles finished grinding the leaves in and brought the bowl to Sonic. "Here."

"Thanks." Sonic took the bowl and drank it. Then his vision started to fog, and everything started spinning. He fell back on the bed, eyes closed.

Knuckles walked through a hole in the rock wall, out into the sunlight. A meadow filled with wild grass and flowers of all colors stretched out toward a dense forest of oak and maple. Tail was walking back with a bucket full of sap. His face was stained red and blue.

"Hey Knuckles. I found a place nearby full of berry bushes. You want to check it out?"

Knuckles sighed. "Maybe later kid. Right now I don't want to let Sonic out of my sight for too long."

Tails looked at the cave entrance. "You think he'll tell someone where we are?"

"Yes, no. Maybe." Knuckles looked out at the forest. Then at the dark clouds. "I don't know. Why'd he have to go and save me? Would've been so much simpler if I knew for certain where he stands." He sat down on a rock.

"You really could've changed?" Tails sat down next to him, handing over the bucket of sap.

"I don't know." Knuckles took a sip from the bucket. "What does he have to gain from tricking us?"

"Do we have any info he wouldn't know?"

Knuckles shook his head. "I doubt it." Then he thought about it. "Wait. Did he mention anything about the chaos emeralds?"

"No." Tails raised an eyebrow. "Why?"

"Just a theory, but I have to wonder." Knuckles looked back at the cave.

-

Part 3

-

Lights flashed on a podium as Chief Oran stepped behind a plastic podium. He pointed at a woman in a green suit with a microphone.

"Chief Oran. What's the status on Sonic the Hedgehog?"

He sighed. "We're still investigating what happened. We don't have any conclusive evidence yet." He pointed to a man in a blue suit.

"Chief Oran. Is there any news on Dr. Robotnick? Will he be releasing any statements in the near future?"

"Dr. Robotnick is working on the situation. You'll hear as soon as we learn anything. For the time being we're still working on finding Sonic and filling the gap in the police force for the time being." Chief Oran pointed to a woman in black suit and sunglasses.

The woman seemed to have a metallic scraping to her voice. Several reporters looked at her raising their eyebrows. "What do you have to say about reports of a robotic machine similar in look to Sonic going about the streets?" Several people murmured before Oran started speaking again.

"That would be Metal Sonic, a prototype police unit robot that's been deemed safe for public use. We've been looking at using Metal Sonic to help with any holes in the police force until Sonic is found. However, it's still questionable how effective it will be in the field." Chief Oran sighed then pointed to a man with a gray trench coat and a fedora.

"And what about the recent break out and explosion at Argon prison?"

"There was only one escapee. A yellow fox with two tails. Luckily the individual in question has only been shown to be a level 1 threat."

The man in the fedora raised an eyebrow. "But footage showed two individuals leaving. And why was a level 1 threat in Argon prison?"

"Someone broke in. And mutant creatures generally are put in Argon until they are shown to be a low level threat. We were actually about to move the prisoner to Mercury." Oran pointed at a woman in a gray skirt.

"What about the footage of the Argon prison escape showing a blue hedgehog?"


	4. Schism

Part 1

-

Protesters filled the city streets with chanting. "Where is Sonic!? Where is Sonic!?" Thousands and people surrounded the Chaos containment center. A line of police blocked the entrance, but didn't seem to be making any arrests.

Hundreds of feet up, chief Oran looked from a window to the people below. He sighed, shaking his head. "This is a disaster." He turned to an opening door behind him.

A woman in what looked like a black wetsuit with plastic armor covering her torso. She walked into the room. "Sir. We've managed to track down Rouge. She's taken the job."

Oran sighed with relief. "Well, at least that should help. Thank you Kya. What's her asking price?"

"10,000 rings." Kya said.

He sighed. "Yeah, I figured as much. Tell her she has a deal. 1,000 in advance, 9,000 when she brings in Sonic."

"And what of Knuckles and the yellow fox?"

Oran turned to the window again thinking. "There'd be even more outrage if we harmed someone with a mostly clean record. Capturing the fox is ideal, but it'd be better to let it go than to harm it.Tell Rouge she'll get a 2,000 ring bonus if she kills or captures Knuckles. But tell her that harming the fox in any way will terminate her reward."

"Very well sir. And what about the fail safe?"

"Tell Dr. Robotnik he'll get whatever he needs." Oran thought for a moment. "Now that you mention it. He said he'd need someone specializing in stealth." A grin formed on his face. "You think you and Percy have what it takes to sneak by Sonic's detection systems?"

"I believe so sir." Oran felt a blade at his neck.

Kya put a dagger in her belt and Oran smiled rolling his eyes. "Show off."

-

Part 2

-

A man in a black combat suit held a remote in his hands. "So this thing can really shut down Sonic?"

Dr. Robotnick nodded. "Yes. But you have to get within 500 meters."

"500 meters? That doesn't sound too hard. Why do you sound so concerned?" The man raised an eyebrow.

"I really hope it is that easy. But by the time you saw him, you'd still probably be close enough for him to attack you before you press the remote. Just be careful." Robotnick picked up Metal Sonic's removed outer shell, sticking his hand through a hole. "That shell here is made of titanium with a maximum shear modulus of 39 gigapascals. That's nearly 1,000 times stronger than human bone. And some new friend of Sonic's managed to bust this hole through it with his bare hands. Percy, just be careful"

Percy gulped, then smirked. "All right. Don't worry Doc. I'll be careful. Remember, I'm the guy who snuck into Fandango and rescued those hostages. They won't even know I was there."

"Well, we should have a fail safe with a 50 km range working within a couple weeks. So don't take any unnecessary risks."

"Right." Percy stepped into a slender black car with blue and red lights on the top. He looked in his rear view mirror, then at a woman in an identical battle suit. "You ready Kya?"

"Yeah. Kya nodded, turning the ignition key. The car roared to life and shot down the street.

Percy looked at a screen showing the roads.

-

Part 3

-

The wind sent a chill through Sonic as he stepped out into the sunlight. He stretched out his arms and legs, smelling the fresh flowers. Knuckles frowned at him. "This is one of the few places you guys haven't destroyed."

Sonic looked at the field, then raised an eyebrow at Knuckles. "What are you talking about? Conservation areas are all over the place. I see them all the time, even the city roads are algae."

"Yeah. With people all over them disturbing the wildlife. You trample the grass so it can't grow and turns brown, dig up everything until the ground collapses, and destroy everything you touch." He looked at the flowers, then back at Sonic. "Do you have any idea how many friends I've lost because of you and the humans?"

Sonic's face dropped as he clenched his fists. Then he relaxed. "I don't think we've destroyed as much as you think. But, you're right about one thing." He paused for a few minutes. "I can't bring her back. I know apologizing won't fix what happened, but maybe I can start doing something."

"Yeah, you can." Knuckles threw him a rolled of paper.

Sonic caught it reading a building plan. "What's this about?" He looked over the plans. They included movable walls, security cameras, electric current running along the floors. "Wait, this is GUN headquarters."

Knuckles nodded. "Yeah. They've been messing around with nuclear weapons, blowing holes in an island chain just off the coast."

Sonic shrugged. "Ok, I mean that sounds bad, but why do you care so much?"

"We're gonna blow up their headquarters." Knuckles smirked.

"What!?" Sonic stared at Knuckles. "There are people in there!"

"Yeah, and they'll finally pay for what they've done."

"Are you insane!? They'll get hurt, maybe even killed!"

Knuckles grimaced. "And my friends will finally be avenged. You want to prove you're one of us now, then help me bring justice to the monsters who are destroying everything."

"No." Sonic said.

"No?" Knuckles frowned, then a smile formed on his face. "Well, at least I know where you stand now." He punched the air where Sonic had been.

Sonic shook his head. "Look, I want to help. But I'm not killing anyone. No matter what they've done, or what's at stake, that's a line I won't cross."

Knuckles punched again. Sonic caught his wrist, throwing him to the ground. Knuckles stood up glaring at him. "Fine. Have it your way. But if we don't stop them, a lot of my friends will die. And their blood will be on your hands."


	5. Tracked

Part 1

-

The car windows rattled in the wind as Percy and Kya rode across the land. The passing roads were a blur of gray, green, and black. Percy watched the radar for Sonic's location. He was moving, but not very fast. "Something doesn't seem right. Sonic never runs this slow, and the way he's moving, it doesn't make any sense." He looked at the screen as it showed the path he'd taken, it was jagged, following the ground as it sped up and slowed down at seemingly random times. It also looked like he was moving back and forth.

Kya kept her eyes on the road. "Where to?"

"It looks like it's down the valley." Percy pointed to a cliff on the side of the car. "But that means his tracker's in the river."

"So he removed it?" Kya shuddered. "Didn't think he had that high a pain tolerance."

"Either that or he's trying to throw us off." Percy said.

"Guess there's only one way to know." Kya did a u-turn, stopping to let Percy out. Then she drove downriver, until she'd passed the location of the tracker by 500 meters. She stopped the car and stepped onto a dry plateau. Kya pulled out her phone and a pair of binoculars, as she looked over the side of a cliff stretching down to the river. "No sign of Sonic here. Percy, have you spotted him yet?"

"No. But I'm closing in." Kya waited for about a minute watching for Sonic before her phone spoke. "I'm right next to the tracker, but I don't see him. I can see you though. Do you see him anywhere?"

Kya looked around seeing Percy in the distance. "No…" She noticed a small glow in the river. "Hold on. I think I spotted something." She climbed down the cliff to get a closer look.

"Kya, what are you doing!?"

"He can't swim. I think I might've found the tracker floating in the water." She climbed down as for a few seconds before hearing Percy.

"Yeah. It's the tracker." Kya reached the bottom and Percy handed her a plastic square chip with lines of metal running along it. A small light bulb blinked brightly at its center. She looked up at Percy who shook his head sighing. "Guess we should get back to headquarters."

Kya spoke into her phone. "Chief Oran." It rang for a few seconds before picking up. "Sir, we just found Sonic's tracking chip floating in the river."

"He did huh?" Chief Oran said. "Guess I should've figured. All right. Good work. Get to safety immediately."

"Copy that sir. We're returning to headquarters now." Kya hung up the phone. Then she and Percy started their climb up the cliff.

-

Part 2

-

"Knuckles. Tell me you're not gonna blow a bunch of people up." Tails said.

"You told him?" Knuckles raised an eyebrow at Sonic for a moment, then shrugged facing Tails. "We're doing what we have to."

"But hundreds of people will die!" Tails yelled. "Even Sonic never went that far."

"Tell that to Cream." Knuckles glared at Sonic, who looked down at the ground. The Echidna turned back to Tails. "Look, Tails, these are bad people. They have this coming. We're not gonna hurt any innocents."

"I thought you said you don't kill. Didn't you say that's what makes us better than them!" Tails turned away, flying toward the trees with his tails.

"Tails! Wait!" Knuckles chased after him, but Sonic stopped him. "Let go of me!"

Sonic shook his head. "He just needs some time to cool off. He'll come back." Sonic looked over at the forest. "But he's right. That's going too far."

"Not this again. What makes you think you can act all high and mighty." Knuckles walked away, then stopped. "Not that I need your help. But the offer's still open if you change your mind."

"Where are you going?" Sonic asked.

"To break your girlfriend out of prison." Knuckles turned back to Sonic smirking. "You down for that?"

Sonic shuddered for a few seconds then sighed. "Guess we had to do that eventually." He looked at the forest then followed Knuckles. "So, what's the plan?"

Knuckles laughed. "Oh, you'll love this one." He picked a flower from the field. "I just need a little distraction. Then I'll handle the rest."

-

Part 3

-

Dr. Robotnick soldered a computer chip, working the metal lines into the green plastic. After a few minutes of work he cleaned the pen before turning off the heat. He wiped the sweat off his forehead and grabbed a cup of coffee. As he drank he looked at his smirking assistant.

"You know. We have machines for that." James rolled his eyes.

"True." Robotnick winked. "But machines have limits. There's only so much detail they can place in a pattern. Sometimes you need a human touch." He looked over the lines of gold in the chip.

"Yeah, and the most expensive metal on the planet." James threw him a gray remote.

Dr. Robotnick caught the remote and planted the chip inside. "What do you want me to do? We can't afford for this to corrode."

"But it'll just shut down Sonic. We don't need it to last that long." James raised an eyebrow. "You don't think it'll take that long for this to work do you?"

"I'm not sure of anything. I designed Specimen 343 to be unstoppable." Robotnick sighed. "And now one of my inventions is on the loose: breaking out prisoners and causing all sorts of chaos. Not to mention the PR nightmare Oran's having to deal with."

"We'll fix it." James placed his hand on Robotnick's shoulder. "Like we always do."

"Yeah. You two are wizards, aren't you?" The two turned to see Sonic leaning against a computer and drinking from Robotnick's coffee cup.


	6. Breakout

Part 1

-

Wind blew across a field of flowers, breaking the silence. Tails stared at Knuckles before speaking. "You promise you won't kill anyone?"

Knuckles nodded. "I won't kill anyone while we're out there. Not today anyway."

Sonic shrugged. "I guess I can live with that. Tails, Knuckles has a plan to rescue Amy. But we need your help."

"I trust Knuckles to keep a promise. As for Sonic." Tails turned to Sonic. "I know you did a lot of bad things, but you rescued me. So you can't be that bad."

Sonic's face changed, like a load had been lifted off his shoulders. Knuckles nodded. "All right. Here's the plan. Sonic's gonna distract the guards by breaking into the police headquarters, while you mess with the security system. That's when I go in and rescue Amy. Then we shut off the electricity. I just need a second to open the door to Amy's cell. An emp should do the trick."

Sonic raised an eyebrow. "Yeah about that. How do you plan to get an emp?"

"Yeah. I'm still working on that. You have any ideas?" Knuckles said.

Sonic thought for a moment. Then his eyes lit and he snickered. "You know. I just might." He looked at Knuckles a little embarrassed. "Though I might need you to bail me out."

"If this works. I think Amy and I can get you out of there no problem. We just need Tails to help us escape out the door." Knuckles turned to Tails. "Can you handle that."

Tails looked uncertain. "Maybe. I'll let you know when I'm ready. But this is a pretty big risk."

Sonic closed his eyes. "Sometimes that's just what it takes."

"All right." Tails nodded. "I'll do what I can."

-

Part 2

-

A pink hedgehog sat in a room lined with metal walls. The only exception was a glass wall with a door locked with an electric panel. Several people in lab coats. Every so often one would point some sort of laser at her and write something down. She'd been in here for 8 months, with no one to talk to. Her hair was a mess, her clothes were covered in filth, and she hadn't been able to take a bath the entire time. She was caged like an animal. She was even given a food and water bowl like some sort of pet. She could feel her sanity slipping away every day, but all she could do with sit. She'd tried escaping, but it never worked. At first she always looked out the glass wall, hoping something would change, that someone would come. But they never did. She just sat on the floor of an empty room, staring a metal wall.

She knew it'd just be a matter of time before she started hallucinating. And today seemed to be that day, because she could've sworn she heard Knuckles. But she knew that couldn't be right. He couldn't break in here, and he was probably dead by now anyway.

"Hey Amy! Are you listening to me!?" Knuckles voice rang through her ears again. But she knew it wasn't real.

"Oh hello Knuckles." Any sighed. "I supppose you've come to rescue me." She laughed, what a joke. That Knuckles would be here. Next thing you know, Sonic would show up.

Knuckles yelled at her. "Hey! Look at me will you!?" Knuckles voice rose further as Amy sat there. "Do I have to drag your sorry butt out of there! Come on!"

Amy felt a hand on her shoulder. She turned to see a red echidna in front of her. He Was this real? She gaped for a few seconds before her wrist was pulled over his shoulder. Knuckles grumbled. "Come on! Even Sonic's more useful than you right now!"

Nope, definitely hallucinating. There was no way Sonic was helping her escape. "Yeah. Ok. Sure."

Knuckles voice changed. "Hey Amy. Are you all right? You seem...off."

"Just waiting to wake up I." May thought for a moment. "I guess I'll try and enjoy this dream while it lasts." She shrugged, getting off Knuckles.

Knuckles raised an eyebrow, then waved. "Whatever. Just follow me."

"Ok, where are we going?"

"To save Sonic." Knuckles started walking.

Amy shook her head before following. "Sure. Why not?" As she caught both she and Knuckles started running. "So what's the plan?"

"We save Sonic and get out! And don't kill anyone!"

"Right. You want to kill everyone and I'll have to hold you ba...hold up." Any stopped. "What did you say?"

-

Part 3

-

Dr. Robotnick gawked at Sonic for a few seconds before sputtering. "Hey! That's my coffee!" He grabbed the mug out of the air, where Sonic had been. "Smart-Alec hedgehog always trying to annoy me..." He grumbled putting the mug on a table. "What a minute."

Robotnick looked at Sonic who waved at him. "What's up Doc?" The blue hedgehog grinned.

Dr. Robotnick's eyes went wide as he scrambled in his coat. He grabbed black square device with a speaker on the front. He spoke into it as he clicked a button on the top. "Specimen 343 is in the lab! I repeat, 343 is the lab! All security got down here now!" He looked back up at Sonic to see him holding the device in his hands.

Sonic laughed. "Well, I didn't realize soap was so great for talking."

Robotnick looked at his hand, which contained a bar of Sonic brand soap. He sighed, resolving himself to whatever fate was coming. "Why are you here 343?"

Sonic shrugged, a goofy smirk forming on his face. "Can't an old friend stop by to say hello?"

James glared at him. "What are you playing at traitor?" He drew a plastic cylinder from his belt and clicked the top. A blue glow started up, blinking on the cylinder's top.

"Oh, you know. Running around, breaking little kids out of prison." Sonic glared at Robotnick. "You mind explaining why an innocent kid was locked up with terrorists?"

James looked at Sonic raising an eyebrow. "You're kidding right? We can't let experiments like him walk around in public."

Dr. Robotnick nodded. "We don't know what he's fully capable of; he's a danger to society. What if someone got hurt?"

"I wouldn't have a problem with keeping him off the streets. Except you locked him in with some of the worst criminals imaginable." Sonic clenched his fists. "What if they killed him!?"

Robotnick sighed. "The needs of the many outweigh the needs of the few."

"Yeah! The needs of the many. Except he's not really a danger is he? No super strength, or speed, or anything like that. Maybe he can sort of fly and is smart. But that's it! Does that sound like a danger to you!?"

James shook his head. "Someone with that kind of intelligence is too dangerous to be walking around in the open."

"That's what I thought…" The blue hedgehog punched through the table. "You locked him up because you're scared! Of a kid, a little kid! You and everyone else want to just lock up everyone you've experimented on, because it makes you feel comfortable! That's not a need, it's a want!"

Robotnick winced, a pang go guilt running down his neck. He couldn't even bring himself to say anything.

James sighed looking at Sonic. "Fine. I guess we could've let the kid loose, but you're not going anywhere." He threw the cylinder at Sonic.

Sonic's eyes went wide as it flew toward him, blinking blue light. He dashed away, sending a small shockwave and hitting the cylinder. Electricity shot out from it in all directions knocking everyone to the ground. Sonic tried to get up, but his systems weren't working. His core had lost all its charge.

"Now you see what happens to traitors." James got up smiling. He wobbled, but kept his balance. "Now it's time to shut you down for good." He limped toward Sonic, ready to switch him off, when an alarm rang.

James covered his ears yelling. "Argh! What is that!?"

Sonic snickered. "Looks like Knuckles' plan worked.

"What are you-" He turned back to see a red echidna and pink hedgehog. His eyes went wide in terror. "No."

Knuckles cracked his knuckles. "I may have promised not to kill anyone. But I didn't say anything about beating people up."


	7. Shutdown

Part 1

-

Sonic winced looking at James's unconscious body. Knuckles rolled his eyes placing a chaos emerald in his glove. "He'll be fine." He thought for a few moments. "But...he'll probably wish he weren't when he wakes up." He and Amy pulled Sonic up, holding him by his shoulders.

Amy raised an eyebrow at Sonic who chuckled. "Hey, how's it going?"

"Fine I guess. How long until you can walk?" Amy asked.

"Uh, let me check." Sonic did a diagnostic of his systems. The EMP hadn't messed with his organic parts just short circuited his nerves, but his core had been completely drained of energy. He only had his biological power. "My super speed won't work until we get outside and recharge it. But my muscles should be working fine in a few minutes." He turned his neck to look at the destroyed lab around him. Knuckles hadn't killed anyone, but Chaos Control wouldn't be recovering for a long time. He just hoped GUN didn't get called in. That would be a serious problem.

Amy and Knuckles carried Sonic out of the lab as he gave them directions through the building. They went through a few rooms and up a flight of stairs. Then they came to a large room with a desk in the middle. Sliding glass doors sat on the edge of the room leading outside.

Knuckles tried the doors, but they budge. Then he punched them, but didn't make a dent. "Ow!" He shook his hand. "What are these made of?"

Sonic managed to stand up on his own. "Bullet proof glass, they're strong enough to take armor piercing bullets." He looked at one of the security cameras. "Hey Tails."

A voice came from the side of the camera. "Yeah? What's up Sonic?"

"Can you open that door?" Sonic pointed at the glass doors.

"Maybe, but they've got pretty good security. I cracked the rest, but I'm not sure the doors are connected to outside systems. Let me see if I can get a work around." Sonic, Amy, and Knuckles waited for a few minutes before they got a response. "Looks like the doors are a closed system, but I did find an elevator shaft in the building plans. Head to your right, there should still be an old panel."

Knuckles walked over to the panel pulling it off. An empty shoot held a steel rope running through. "Ok, now what?"

"Climb up the steel rope to the next level. Take your first right at room 215. There should be a balcony you can jump from."

Amy nodded. "Will do. Thanks Tails!" The trio climbed the rope and up the shaft to another panel. Knuckles pulled it off and climbed into a metal hallway. He looked to his right and found a door with a red number 215.

The trio went through the door and a security turned toward them. "Hey guys, there's a roof you can jump to from the balcony that should lead pretty close to where I am."

"Right." Sonic waved at the camera. "Stay out of sight until we reach you."

"Can do."

Sonic felt the sunlight hit his face as he walked onto a white tile floor with a metal railing. Knuckles and Amy followed as Sonic stepped onto the rail. He watched Amy and Knuckles jump to a brick roof. He waited a few seconds letting the sun hit him as his systems recharged. Then he jumped, following Knuckles and Amy.

Then his body collapsed. He felt his limbs go numb and his vision went dark. Amy and Knuckles looked back as he yelled. "Ahhh!" Pain ran across his body like an electric shock going down from his head.

-

Part 2

-

Percy and Kya handed Sonic's tracker to Chief Oran in his office. He looked at it for a few moments, weighing it in his hands. "I can't believe Sonic managed to remove this thing without killing himself."

Percy shrugged. "It is what it is. So, what's the plan now sir?"

"Well, for now hold on to Sonic's kill switch, trading it with squadrons 12 and 32, eight hours on and sixteen hours off. Head over to Harold, and you'll get the device back from George. I'll let you know immediately when we get any leads. But hold on a second before leaving." Chief Oran turned to Kya. "As for you, Kya, somethings come up. I need you in Sepview City. The commander of GUN will give you more details. And take the driverless car, I want you rested." He threw a set of keys to Kya.

Kya caught the keys. "Understood sir." She saluted before walking out of the office.

Oran turned back to Percy. "I understand you have some history with Sonic. Any ideas on what his next move might be?"

Percy thought for a few minutes. "Well. I suspect he'll avoid killing anyone if at all possible. Though I suspect you know that too since you haven't called in team X. He's ever really cared about property damage, so it wouldn't surprise me if he attacked some buildings. I'm still not sure why he left though, so it's hard to say what he'll do. Maybe break someone else out of prison? I mean he already did it once. Cheese seems like a possible target I guess."

Oran nodded. "Hmmm. Yeah, I could see that happening. I wonder…" He thought for a few moments. "Oh! Before I forget!" He pulled out a drawer with a few large square batteries. "These should let you use the remote more than once." Oran handed the batteries to Percy.

A voice came from the watch on Oran's wrist. "Sir! We've detected a breach in security!"

Oran and Percy turned to the desk. "What!? Where!?"

"Our entire system's been hacked. And since we lost contact with the lab, we believe that's the source!"

Percy and Oran dashed out of the room and several flights of stairs before coming to the lab. The lights were still on, but everything else was off. There were several researchers lying on the floor unconscious. Others were struggling to move around through destroyed equipment. Several had bruises, but there didn't seem to be a single drop of blood around. He looked at Oran when one of the researchers saw them. "Sir! Sonic broke into the lab with Knuckles and Amy!"

"What!?" Percy pulled out the remote, about to press the button.

Oran stopped his hand. "Hold on. Make sure you're in range. Remember, we've only got one shot before you need to replace the battery." Oran turned to Percy. "Head to front desk. I'll check around back."

Percy nodded, dashing to the front desk with his finger on the button. He went up the stairs, clicking a button on his suit to hide from the security cameras. He came to the front desk and saw a missing rectangle portion in the wall with a steel rope behind it. He checked the rope strength and climbed up to another missing chunk of wall. He swung off the rope, jumping through the hole.

As he landed, Percy saw a typical hallway, but one of the doors was open, room 215. He ran through the hallway as quietly as possible, pulling out the remote again. Then he looked over to a balcony to see Sonic landed on a roof, several meters away. He started running and was getting further and further away before Percy pressed the kill switch.

Sonic collapsed. Percy pressed a button on his watch. "Sonic's on the roof of Stoton 280. He's currently neutralized."

A voice came from his watch. "Copy that. We're already heading that way."

-

Part 3

-

Knuckles looked at Sonic as he fell, struggling to get to his feet. He and Amy ran to Sonic, grabbing him. Knuckles grimaced. "So, the emp hasn't stopped affecting you."

Sonic didn't answer. "Hey!" Knuckles barked. "Sonic! You awake in there!" He looked at Amy. "Sorry, guess we're carrying him back."

Amy and Knuckles carried Sonic as fast as they could across the rooftops before a group of a group of armored officers with guns cut off their path. Knuckles' eyes went wide. "Come Sonic. You better wake up, or we're gonna get killed out here. And they're coming for Tails next."

A woman in black body armor with yellow stripes on her shoulders walked to the front of the officers. "Knuckles and Amy. You are under arrest. Any attempts to resist will result in your deaths."

"Yeah. And what kind of guarantee do I get that you won't kill us the moment we surrender?" Knuckles spat on the ground, feeling a chaos emerald hidden in his glove.

"No harm will come to any of you. We merely wish to keep you from harming others in a safe containment."

Knuckles shook with fury. "Why, so you can scorch the Earth unchallenged. How many more of us are you gonna take away?" He took a few minutes to think. He could use the emerald, but he didn't know if he could avoid killing anyone that way. He was also sworn to protect the planet at all costs, but once more, he shouldn't abuse the power he held now. Did this situation justify it?

Amy nudged him. Her thumb touched her middle finger, with her index pointing at a canopy near the street below. He turned back to the woman. "Well Knuckles, it's your choice. Will you come quietly, or do we have to put you down?"

Knuckles and Amy glanced at each other before jumping off the building with Sonic. They bounced off the canopy and landed on the street. Then they ran as fast as they could.

Knuckles legs burned as he and Amy ran further and further. Then he saw a large river with sides made of concrete. The water flowed out from a pipe up ahead. Chaos control wouldn't follow them into the sewer line and risk poisoning the entire city. Or at least they wouldn't use any weapons in there.

Darkness surrounded Knuckles as he and Amy carried Sonic into the tunnel. He wasn't sure how long it would take to get to Tails, but he had to make sure he was all right. Maybe he could fix Sonic too. Whether Knuckles liked him or not, Sonic was useful. They needed that hedgehog's help, and Knuckles would break all his bones before letting an ally get killed. "Sonic, I'm going to kill you if you let that EMP kill you."


	8. Despair

Part 1

-

Wind blew through the city streets, threatening to blow Percy off the roof as he explained the situation to Chief Oran. "Sonic's operating system is shut down, but his friends took him away."

Oran nodded. "Well, we'll have to fix that later. But in the meantime...well done Percy!" A beaming smile crossed his face.

Percy shook his head. "But sir, Sonic wasn't captured. We can't reprogram him."

"True. But his systems are shut down. He won't be a threat anymore. And that's the important thing for now. It's nice to finally have some good news." Oran turned to face the streets below. "Besides. We know where he's headed. And Metal Sonic is operational again." Oran looked at Metal Sonic as it ran through the streets. It scanned its own systems checking to make sure everything was operating correctly. There were no errors detected.

The sensors ran across the ground and buildings. So far, all detected life forms were human and animal non-variant. None showed significant levels of chaos energy like that in Knuckles, Sonic, or Shadow, but the destination site hadn't been reached yet.

Soon Metal Sonic came to the entrance of the water treatment plant. The robot's parameters demanded that no damage could be done to the treatment plant, and keeping the water safe was the top priority. Secondary priority was recovery of Sonic, followed by capture of any other supernatural animals.

The black streets and metal skyscrapers gave way to smaller buildings, and eventually a concrete canal with a flowing river. Metal Sonic followed the river to a tunnel, entering at top speed. As visible light disappeared, Metal Sonic's systems started sending out small sounds to tell its surroundings by radar. A map of the tunnel system formed in it's database to update the information it already had, but there was still no sign of any life forms. There weren't any detectable sources of electricity or energy nearby either. Soon, Metal Sonic got far enough into the tunnels that it's communication with headquarters was cut off. It could no longer receive orders or send data back. From here on out, it was on its own.

-

Part 2

-

Knuckles and Amy collapsed to the ground as they finally met up with Tails, who had been working on a laptop. It sat on a metal lit by battery powered lamps. Tails looked at Sonic, who still had a heartbeat and was breathing, but didn't react to his name. "Hey Sonic! Sonic! Wake up!"

"He's not getting up." Knuckles heaved between gasped breaths. "Whatever that EMP did to him, it wasn't good."

Tails struggle to lift Sonic onto a metal table surrounded by tools. After visiting the landfill he'd found enough machinery and scrap metal to make a pretty good workshop. He took out a device to check Sonic's systems. It didn't look like any wiring had been fried. For that matter, there didn't even seem to be any damage throughout his entire body. "Huh, that's odd." He kept looking over Sonic's systems.

Amy sat up, managing to somewhat catch her breath. She looked at Tails. "What?"

Tails kept looking over Sonic. "Well...I don't see any damage to Sonic. The organic parts don't seem to have any issues, and neither do his robotic parts. Maybe I'm missing something, but from what I'm seeing, Sonic's fine. So it kind of bugs me that he's not waking up."

Amy thought for a moment. "Well, he did say he'd need some time in the sun to recharge his super speed. Maybe he just ran out of power?"

Tails shook his head. "No, that's not it. He's at well over half power, so he should definitely be able to move around right now." He looked at Sonic's head, there was a latch at the top that looked fairly easy to open. "I wonder…"

Knuckles sat up, a concerning thought came to him. "Tails, you don't think that EMP messed with his brain do you?"

Tails took a scan of Sonic's brain, then shook his head. "No, he's not malfunctioning, and his brain's definitely fine. I don't think that EMP did any real damage. It's almost like he's been turned off, like it's something his systems were meant to do."

"What?" Amy stood up, walking over to Tails. "That doesn't make any sense. You can't just turn someone off." She shook her head. "This is one weird hallucination."

Tails raised an eyebrow at her, then shrugged. "Sonic's part robot, so it makes sense. And on the plus side it means he's not in any danger. Once he turn him on again, he should be fine." He thought about popping the lid on Sonic's head, but stopped. "Problem is, I don't know how to do that, and if I mess up, there's no telling what it'll do to him."

Knuckles sighed. "Well, at least we know he won't die on us. Any idea how it'll take to figure his systems out."

"I'm not really sure. It'll probably take me at least a week, but I doubt it'll take me more than a month. Still, it's hard to say. I'm not really familiar with his design systems. The only thing I have to go on is his coding. I'm just glad I know the programming language already, matlab might be a pain, but at least it works for robotics." Tails' smile faded. "But I don't know how I have to wake Sonic up. Even with his low metabolism, there's a real risk of him dying of thirst or hunger."

Knuckles grimaced. "He might deserve it, but we can't afford for him to die." He looked around the workshop. "I know this is a little sudden, but we should probably get out of here as soon as possible. Do you have any way to move your tools out from here?"

Tails clicked a button. "Yeah. Figured we might need to move. I managed to rebuild some remote control cars people threw away." Several carts came into view. Tails started shoving tools into the carts. "I can get these to follow us anywhere we go."

"Whoa." Knuckles looked at the machines in amazement. "Kid, you're something else."

Tails scratched the back of his head laughing. "Thanks." Then his eyes narrowed at a sound coming down the tunnel. "Hey. Did you guys hear that?"

Knuckles and Amy both nodded. "Yeah." Knuckles turned toward the sound. "You guys wait here. I'm gonna check that out."

Sweat formed on Amy's forehead. "Hey Tails. You wouldn't happen to have my hammer would you?"

Tails shook his head. "Sorry. None of the files I managed to get said anything about your hammer. I have no idea where that might be."

"Yeah I figured." Amy dropped her shoulders. Then she noticed a long pipe like piece of scrap metal in one of Tails' carts. "Hey, you mind if I borrow that?" She pointed at the scrap metal.

Tails pulled out the scrap metal. 'This? Sure." He tossed it to Amy. "Take this too." He threw Amy a construction helmet with a headlamp on it.

She caught both objects, putting the helmet on. Then she felt the metal in her hands. Not quite like her hammer, but the weight and momentum were close enough. "Thanks. I'm gonna go check on Knuckles. I have a feeling those soldiers are catching up to us."

Tails pushed a button on Sonic's metal table. Wheels popped out at the bottom as Tails pulled some belts to strap Sonic to the table. "Then get Knuckles, and we'll ride my carts out."

Amy nodded before running after Knuckles. Then she heard a yell from Knuckles. "Ahhh!" The sound echoed through the tunnel as Amy got closer and closer. Then she saw him. "Knuckles!" Knuckles was still standing, but his right shoulder had swelled into a purple balloon. Blood dripped from his mouth as he faced off against what looked like a robotic version of Sonic, its eyes glowing red. A small tear in it's armor showed blue sparks of electricity.

The robot turned to face Amy, and Knuckles threw a left hook. The robot dodged, and threw Knuckles into the wall. It went to ram him, but Amy smacked it away with her metal rod. The rod bent, but the robot had a dent to match, right on its head. Amy felt the vibration through her hands, barely able to hold onto the rod. As the robot recovered, it charged Amy with its wheels screeching.

She aimed her rod, throwing it like a javelin. The rod hit the robot, shattering as shrapnel flew across the tunnel. For a few seconds, Amy couldn't see anything. There was nothing but silence. Then she was able to see the robot. It wasn't moving, a gaping hole in its chest, and its eyes gone dark. Amy grabbed Knuckles and helped him stand. "Come on. Let's get out of here."

Knuckles gave a grunt, but nothing else. Then Amy put him on her shoulder, running after Tails.

-

Part 3

-

Dr. Robotnick looked over a file on Sonic's code. He hadn't considered it before, but he should probably have a system in place to immediately reprogram Sonic on retrieval. That fox child had already managed to hack into the security system. He might be able to restart Sonic too. After all, the fail safe was never designed to kill Sonic. That would raise too many questions. He had to make sure Sonic wouldn't hurt anyone. Still, something felt wrong as he coded Sonic's new program. Sonic was part robot certainly, but he wasn't just that. Reprograming Metal Sonic was one thing, it was just a machine, but Sonic was alive. Was it right to take away someone's free will, even if they were threatening others?

He sighed, trying not to think about it too much. Robotnick turned to his assisstant James as he worked on an increased range for Sonic's failsafe. "What's your current estimate for the fail safe's maximum distance?"

James turned to Robotnick. "Well, there are two designs that I have right now. One will take about two weeks to build, and has a range with a radius of 2 kilometers. The other is twice as expensive and will take about a month to build, but has a range with a radius of 20 kilometers. They also can send a constant signal, but aren't portable."

Robotnick nodded, taking a sip of coffee. "That should at least keep him from causing any trouble in the city." He sighed. "It's sad that it's come to this. I wish there was another way."

"Traitor's brought this upon himself. We're just defending ourselves and the city." James looked over the designs to the two fail safes. Both showed blue outlines of a sattelite dish against a black background. He looked at the design. "Hopefully Metal Sonic can bring him in. I'd rather not take up too much of the police budget."

Robotnick kept looking through Sonic's code, making edits where he thought it made sense. Then he came across that made him hesistate. He could add a set of command codes that would routinely erase any thoughts and memories that would make Sonic turn against Chaos Control. He'd already written the coding along time ago, but he hadn't added it to Sonic's systems. He weighed his options, but even after a few minutes of thought, he still couldn't decide what to do. He moved on to other parts of the code, as he kept thinking about the command codes.

He kept working and thinking. Then an idea came to him, a clone. If he could grow a clone with Sonic's memories up until that child died. What was her name again, Cream? Robotnick had suspected that had messed with Sonic, he wasn't the same after, and the changes showed strongest right before he went rogue. There had to be a connection. Maybe he could make a new code that could just keep him from remembering events of that magnitude. Designing a code with that much detail would take, so he'd have to focus on that for a while. Then he'd focus on an internal kill code, one that would shut him down if his loyalties ever changed. Back when he'd first built Sonic it didn't seem necessary, now he knew better. Whatever it took to protect the city, he would do it. As he worked on the code, a dull pain filled his heart. His stomach turned thinking about what he was doing, and tears started forming on his eyes.

A single whimper came from Dr. Robotnick before he managed to force his mouth shut. James turned to him to see the tears in his eyes. "Hey, what's up Doc? You get something in you eyes?"

Robotnick shook his head, trying to keep his voice level. "It doesn't matter. I've already made up my mind to go through with it." His voice dropped to a whisper. "I'm sorry Sonic..."

James looked at the old roboticist. He couldn't tear his eyes away from the Robotnick's shivers. "I'd tell you it's for the greater good, but I doubt that'd help. I'm sorry you're the only one who knows his code well enough to do this. I can't imagine what it'd be like to hurt anyone in my family."

"343's not family." Robotnick gritted his teeth, trying to ignore the pit in his stomach.

"Yeah he is." James truned back to the designs. "What else do you call someone you raised from birth?"


	9. Meanwhile

Part 1

-

A black car with 1 way windows stopped in a quiet neighborhood. Green grass blew in the wind around sidewalks made of sand and dirt. Houses of different colors dotted the side of the algae road way. The steep roofs shot into the sky, daring rain and snow to test their might. But in the starless night sky, not even a single cloud flew overhead. Only the crescent moon shown, leaving the streets in darkness.

The darkness only grew with the black car's headlights turning off. The purr of its engine stopped, and the door opened as Dr. Robotnick stepped out. He walked to his mailbox pulling out a letter that caught his attention with its handwriting. A small smile formed on his face, when he noticed a figure approaching in the distance. He saw a young boy walking a scruffy brown dog. Next to the boy, a balding man with gray hair waved at Robotnick.

Robotnick turned to the man. "Thornjaw. How are you?"

"Well, I suppose I'm all right. Though my family's been in an uproar lately. Can't get two words in without someone mentioning Sonic's disappearance. Least of all my grandson." Thornjaw smirked at the young boy who rolled his eyes. "How about you Ivo?"

Robotnick sighed. "Well, work is work I suppose. Though it's certainly been a little more stressful lately." He chuckled to himself holding up a letter. "At least I have something good to make my day."

Thornjaw looked at the letter, recognizing the handwriting. "So, your eldest finally decides to write. How is Shadow anyway?"

Robotnick rolled his eyes. "You know as well as I do. I know he's busy keeping the world safe, but I'd appreciate getting to talk to him every now and then. Maybe I should give him a call." He tucked the letter into his pocket heading for his house.

"Well then I won't hold you up, have a good night." Thornjaw and his grandson kept walking.

Robotnick glanced back before pulling out a circular key and unlocking his front door. He stepped inside, placing his red trench coat on a wooden coat rack. He walked into the living room and made his way to the kitchen. He sat at a table in the kitchen opening the letter.

Dear Ivo,

Hope everything's going well. Sorry I haven't written or called recently. We've been working in hostile territory for the last month and couldn't use phones at all. Things have gotten crazy, but nothing I can't handle. Actually, I get some leave time at the end of the month, so I'll have a chance to visit.

Shadow

P.S. Tell Sonic I said hi. Don't tell him I said this, but I have missed that blue fur ball.

As Robotnick looked at the letter he went from rolling his eyes to excitement. But by the end, his face had grown grim, feeling as though he were aging years within the span of two sentences. He tried thinking to himself how he'd explain his actions, and what he needed to do to keep the city safe. But the more he thought, the more he hated himself. He turned to a window showing his reflection, and he wanted to shatter it, break it into a million pieces so he didn't have to look at himself. What was he doing? Could he really do this to his own family? Sonic hadn't been captured yet, so he didn't have to do anything yet. But it was only a matter of time. Sooner or later he'd be forced to take away Sonic's free will, even if just partially. What he'd be doing was the greatest betrayal of all. He tried to deny it, but James was right. Sonic was his family.

-

Part 2

-

A white bat-like creature glided through the night sky. Night vision goggles helped it view the surrounding ground to spot her target. He had to be down there somewhere. Based on the intelligence she'd gathered, there was nowhere else Sonic could be. His systems gave off a surprisingly easy to track signal. How Chaos Containment hadn't captured that hedgehog, was behind her. But Rouge wasn't about to complain about a high payday, even if her target was as dangerous as she thought.

She didn't believe those stories though. Someone breaking the sound barrier and surviving a 10 story drop were hard enough to believe, but single handedly taking down a terrorist organization was ridiculous. Still, rumors had to come from somewhere. Some might be entirely made up, but some likely had some truth. After all, she had seen him outrun a police squadron car, and his skill with martial arts was concerning as well.

There was also the concern with Knuckles. That anarchist might not be that bright, but his strength was still a threat. His resourcefulness also needed to be exceptional to avoid arrest for so many years. Hopefully she could avoid him, but his bounty made it worth nabbing him too. Not that she'd be able to take on 2 fighters of at least level 2 threat level. Sonic was probably closer to level 5, but she didn't think he'd be any higher than a level 6. He wasn't Shadow after all. A fight with that monster would be suicide, she just had to hope Shadow didn't come after her for this. For a moment she had second thoughts about going after Sonic, but as long as she didn't break any laws Shadow wouldn't have any excuse to come after her. Besides, he was thousands of miles away.

For now she just had to focus on finding Sonic. He'd started giving off some weird readings on her trackers, but there was no doubt it was him. No one had energy like Sonic's except Amy, but she was still locked up. Knuckles seemed to have the same energy as she'd expected, but there was another energy signature that bothered her. It wasn't very strong, but any level of chaos energy was concerning.

Rouge dove down through the clouds to get a better view of the rocky hills below. The tracker showed the life signs were close enough that she should be able to see them fairly soon. Then she found herself getting further away from them. She circled around, and kept following the tracker, but as she got closer and closer to the ground, something felt off. They were almost directly below her, but further away than the ground. "What in the world? How did they get underground?"

Rouge landed before checking around for any caves nearby. If they were in caves, then it made sense for Sonic and his new partner in crime to feel safe. Maybe it was possible they'd have their guard down and she could take them down in their sleep. That was a dangerous line of thought though, she had to be ready for a fight.

She clicked on the side of her goggles making a screen pop up. Her scanner had made a map of the area and there seemed to be several caves nearby. Rouge flapped her wings just enough to get airborne before gliding over to the nearest cave entrance she'd fit through. She turned a dial on her watch to amplify any sounds coming from the cave. The device made the sound of wind and dripping water, but there weren't any voices. She went over to another entrance, then another, checking for any sounds of sentient life.

After 3 hours of searching, there was no sign of her targets. Rouge felt her eyes drooping a little. Even if she managed to find Sonic right now, she wouldn't be able to fight him. She tapped the device on her wrist, setting up an alarm. Then she lay down in a soft dry patch of dirt. She could keep searching for her targets later, once her strength was back.

-

Part 3

-

As the rising night sky cast a massive canyon in shadow, 3 figures stood at the edge of a 100 meter tall cliff: Shadow, Silver, and an echidna with pink and orange fur. They turned on their night vision goggles, checking their surroundings for any threats. Shadow, a hedgehog with black fur covered in red lines, nodded to his companions to make sure their timing was synced. His piercing eyes glowed with a dim red light of solemn determination as the trio jumped into the abyss below. Silver, a silver hedgehog, shot a green light from his hands. As the light surrounded the 3 figures, their fall slowed before they gently landed on the bottom of the cliff.

Shadow looked at his companions, motioning with 2 fingers toward a massive, granit archway. Carvings lined its entire length, glowing with pink energy. The trio went through the archway, entering a sprawling cavern lined with glowing crystals and mushrooms that seemed to suck in any light around them like black holes. The cavern stretched out of sight as the trio ran through. As they went further and further, a low hum became audible. Shadow and Silver tensed as they got closer, but the third figure was shivering.

The hum got louder and louder as a pale blue glow appeared. It reached across the cavern walls growing brighter and brighter as the trio got closer. Their goggles adjusted for the light change as they saw a two-legged creature made of clear liquid, the source of the light. It had a chaos emerald in each of its shoulders. Its forked tail wrapped around a chaos emerald on a metal stand in the center of the cave. As the trio approached the creature absorbed the chaos emerald, its blue light growing brighter. The emerald appeared in the creature's chest as the light faded.

It turned toward the trio with an ear splitting screech. "Eegh!" The trio covered their eyes, except Shadow who ran at the creature. A sonic boom exploded behind him as he shot into the creature. The creature stretched out in a hole, letting Shadow fly through. Shadow stopped just short of the cave wall as Silver caused rocks from the caves to shoot at the creature. It dodged left and right, morphing into different shapes and sometimes letting itself get hit. The rocks aimed for the chaos emeralds, but kept missing.

Shadow ran at the creature, stopping right in front of it. He punched the creature over so fast, his movements blurred. Ripples and bubbles formed on the creature as its body vibrated back and forth. The creature's chaos emeralds stopped moving as quickly the rocks started hitting them.

The emeralds looked ready to come loose when they started glowing. The rocks started bouncing off the creature, and its ripples disappeared. Energy blasted Shadow back as the creature screamed again, sending everyone even Shadow to the ground. The chaos emeralds grew brighter and brighter as the screaming got louder and louder. A blinding light filled the cave and the creature's screams died away.

It sagged trying to keep its form intact as Shadow yelled. "Tikal! Now!"

Tikal, the echidna, thrust her hands out, sucking the creature into a jewel on her neck. The creature pulled back and Tikal fought to suck it in. Silver and Shadow attacked the creature, sending its emeralds flying. Then, the creature was gone, sucked into the jewel.

Tikal fell back into Shadow's appearing arms. She forced a whisper out. "Five minutes..." Shadow nodded, picking her up and shooting out of the cave. Everything blurred around as he ran faster and faster the landscape and even climate changing around him: brown to blue, hot to cold, dry to wet.

As he kept going he counted the time in his head: 3 minutes, 2 minutes, 30 seconds. He stopped at the top of a staircase, laying Tikal on the ground. She struggled to keep conscious as Shadow spoke. "Come on. One more step."

Tikal forced herself up, looking at an enormous green chaos emerald. Putting her hands out, she drew from its power, sending the creature into the massive emerald. Then, she let herself fall asleep.

Shadow lay her down gently breathing a sigh of relief. He pressed a device on his ear. "Agent Shadow reporting. Chaos has been contained."


End file.
